Figure 2 Genomic map of a member of the genus Potyvirus, using a strain of Tobacco etch virus as an example. The ssRNA genome is represented by a line and an open box representing the ORF translated into a polyprotein. Functions associated with the mature proteins proteolytically processed from the polyprotein are shown. VPg, genome-linked viral protein covalently attached to the 5′-terminal nt (represented by the oval at the 5′ end); P1-Pro, a protein with a proteolytic activity responsible for cleavage at typically Tyr/Phe-Ser (◯); HC-Pro, a protein with aphid transmission helper-component activity and proteolytic activity responsible for cleavage at typically Gly-Gly (◆); Pro, serine-like proteolytic activity responsible for cleavage at Gln/Glu-(Ser/Gly/Ala) (▼). Some of these proteins of particular viruses of the family Potyviridae aggregate to form inclusion bodies during infection. The protein involved and the particular type of inclusion body is shown above the genetic map; AI, amorphous inclusion; CI, cylindrical-shaped inclusion body found in the cytoplasm; NIa and NIb, small and large nuclear inclusion proteins, respectively, which aggregate in the nucleus to form a nuclear inclusion body. The small ORF PIPO is putatively translated by +2 frameshift of the polyprotein ORF, and its product is expressed as a fusion with the N-terminal part of P3.

Figure 3 Genomic maps of the ipomoviruses sweet potato mild mottle virus (SPMMV), squash vein yellowing virus (SqVYV) and cassava brown streak virus (CBSV). The ssRNA genome is represented by a line and an open box representing the ORF translated into a polyprotein. Conventions are as for the potyvirus genome organization map (Figure 2). Activities of most gene products are postulated by analogy with genus Potyvirus. CVYV and SqVYV contain two P1-like serine proteases (P1a and P1b), of which P1b functions as a suppressor of RNA silencing. CBSV also contain P1b which suppresses silencing and, additionally, carries a Maf/HAM1-like sequence recombined into the NIb/CP junction. HAMh1 might intercept non-canonical NTPs to reduce mutation rates of viral RNA.

Figure 5 Genomic map of the bymovirus bipartite genome, using, as an example an isolate of barley yellow mosaic virus. Conventions are as for potyvirus genome organization map (Figure 2). Function of most gene products are postulated by analogy with genus Potyvirus. P1 corresponds to the C-terminal protease of HC-Pro.

Figure 6 Unrooted phylogenetic tree based on the codon-aligned nucleotide sequences of the polyproteins of fully-sequenced members of the family Potyviridae. The tree uses the majority of the polyprotein (from the 6K1 cistron to the end of the coat protein). One representative sequence was chosen for each species. The analysis was done in MEGA4 (maximum composite likelihood distances) and the numbers on major branches indicate percentage of bootstrap support out of 10,000 bootstrap replications.

Figure 7 Phylogenetic (distance) tree based on the codon-aligned nucleotide sequences of the 3′ ends (partial NIb and complete coat protein) of the polyproteins of members of the family Potyviridae. The analysis was done in MEGA4 (maximum composite likelihood distances) and the numbers on branches indicate percentage of bootstrap support out of 10,000 bootstrap replications (where >60%). Because of the large number of sequences in the genus Potyvirus, the branch for this genus (and Rymovirus) has been collapsed. The tree is provided particularly to demonstrate the position of unassigned members of the family and those in the genus Macluravirus, where complete sequences are not available.